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Time stepping

Skill BioTender-max/awesome-bio-agent-skills/skills/openclaw/time-stepping

A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.

Install
npx -y skills add BioTender-max/awesome-bio-agent-skills --skill time-stepping

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Plan and control time-step policies for simulations. Use when coupling CFL/physics limits with adaptive stepping, ramping initial transients, scheduling outputs/checkpoints, or planning restart strategies for long runs.

SKILL.md

4.4 KB, ~1.1k tokens by cl100k_base, as published. Nobody here has run it

Time Stepping

Goal

Provide a reliable workflow for choosing, ramping, and monitoring time steps plus output/checkpoint cadence.

Requirements

  • Python 3.8+
  • No external dependencies (uses stdlib)

Inputs to Gather

InputDescriptionExample
Stability limitsCFL/Fourier/reaction limitsdt_max = 1e-4
Target dtDesired time step1e-5
Total run timeSimulation duration10 s
Output intervalTime between outputs0.1 s
Checkpoint costTime to write checkpoint120 s

Decision Guidance

Time Step Selection

Is stability limit known?
├── YES → Use min(dt_target, dt_limit × safety)
└── NO → Start conservative, increase adaptively

Need ramping for startup?
├── YES → Start at dt_init, ramp to dt_target over N steps
└── NO → Use dt_target from start

Ramping Strategy

Problem TypeRamp StepsInitial dt
Smooth ICNone neededFull dt
Sharp gradients5-100.1 × dt
Phase change10-200.01 × dt
Cold start10-500.001 × dt

Script Outputs (JSON Fields)

ScriptKey Outputs
scripts/timestep_planner.pydt_limit, dt_recommended, ramp_schedule
scripts/output_schedule.pyoutput_times, interval, count
scripts/checkpoint_planner.pycheckpoint_interval, checkpoints, overhead_fraction

Workflow

  1. Get stability limits - Use numerical-stability skill
  2. Plan time stepping - Run scripts/timestep_planner.py
  3. Schedule outputs - Run scripts/output_schedule.py
  4. Plan checkpoints - Run scripts/checkpoint_planner.py
  5. Monitor during run - Adjust dt if limits change

Conversational Workflow Example

User: I'm running a 10-hour phase-field simulation. How often should I checkpoint?

Agent workflow:

  1. Plan checkpoints based on acceptable lost work:
    python3 scripts/checkpoint_planner.py --run-time 36000 --checkpoint-cost 120 --max-lost-time 1800 --json
    
  2. Interpret: Checkpoint every 30 minutes, overhead ~0.7%, max 30 min lost work on crash.

Pre-Run Checklist

  • Confirm dt limits from stability analysis
  • Define ramping strategy for transient startup
  • Choose output interval consistent with physics time scales
  • Plan checkpoints based on restart risk
  • Re-evaluate dt after parameter changes

CLI Examples

# Plan time stepping with ramping
python3 scripts/timestep_planner.py --dt-target 1e-4 --dt-limit 2e-4 --safety 0.8 --ramp-steps 10 --json

# Schedule output times
python3 scripts/output_schedule.py --t-start 0 --t-end 10 --interval 0.1 --json

# Plan checkpoints for long run
python3 scripts/checkpoint_planner.py --run-time 36000 --checkpoint-cost 120 --max-lost-time 1800 --json

Error Handling

ErrorCauseResolution
dt-target must be positiveInvalid time stepUse positive value
t-end must be > t-startInvalid time rangeCheck time bounds
checkpoint-cost must be < run-timeCheckpoint too expensiveReduce checkpoint size

Interpretation Guidance

dt Behavior

ObservationMeaningAction
dt stable at targetGoodContinue
dt shrinkingStability issueCheck CFL, reduce target
dt oscillatingBorderline stabilityAdd safety factor

Checkpoint Overhead

OverheadAcceptability
< 1%Excellent
1-5%Good
5-10%Acceptable
> 10%Too frequent, increase interval

Limitations

  • Not adaptive control: Plans static schedules, not runtime adaptation
  • Assumes constant physics: If parameters change, re-plan

References

  • references/cfl_coupling.md - Combining multiple stability limits
  • references/ramping_strategies.md - Startup policies
  • references/output_checkpoint_guidelines.md - Cadence rules

Version History

  • v1.1.0 (2024-12-24): Enhanced documentation, decision guidance, examples
  • v1.0.0: Initial release with 3 planning scripts

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